I can see a base "normal paint" Model Y coming from Fremont. Non-metallic black, white, or grey.
While the 3 layer paint from Austin is sold at an upcharge.
They can adjust relative prices to get the relative orders correct for the capacity they have at Fremont/Austin.
That said, the S & X are exclusive to Fremont, and they surely deserve both better paint and better paint options as well. I suspect once Austin is operational, and Tesla can meet some of their delivery goals there... maybe they disassemble / upgrade Fremont paint shop for S3XY. But there's no way they can do that now, as it'd shut down production.
How many weeks would it take (if they worked 24/7) to install an upgraded Fremont paint shop? I'd suspect 2022 at the earliest for this.